CeleScope Report

Chemistry : For more information, see here.

Raw Reads : Total reads from FASTQ files.

Valid Reads : Reads pass filtering(filtered: reads without poly T, reads without linker, reads without correct barcode or low quality reads).

Q30 of Barcodes : Percent of barcode base pairs with quality scores over Q30.

Q30 of UMIs : Percent of UMI base pairs with quality scores over Q30.

Reads with Adapters : R2 reads with poly A(read-through adpaters) or sequencing adapters.

Reads Too Short : Reads with read length less than 20bp after trimming.

Reads Written : Reads pass filtering.

Base Pairs Processed : Total processed base pairs.

Base Pairs Quality-Trimmed : Bases pairs removed from the end of the read whose quality is smaller than the given threshold.

Base Pairs Written : Base pairs pass filtering.

Uniquely Mapped Reads : Reads that mapped uniquely to the genome.

Multi-Mapped Reads : Reads that mapped to multiple locations in the genome.

Feature Type : Specified by `--gtf_type`. For snRNA-seq, you need to add `--gtf_type gene` to include reads mapped to intronic regions.

Reads Assigned To Exonic Regions : Reads that can be successfully assigned to exonic regions.

Reads Assigned To Intronic Regions : Reads that can be successfully assigned to intronic regions.

Reads Assigned To Intergenic Regions : Reads that can be successfully assigned to intergenic regions.

Reads Unassigned Ambiguity : Alignments that overlap two or more features.

Estimated Number of Cells : The number of barcodes considered as cell-associated. The cell calling method used for this sample is auto.

Fraction Reads in Cells : The fraction of uniquely-mapped-to-transcriptome reads with cell-associated barcodes.

Mean Reads per Cell : The number of valid reads divided by the estimated number of cells.

Median UMI per Cell : The median number of UMI counts per cell-associated barcode.

Total Genes : The number of genes with at least one UMI count in any cell.

Median Genes per Cell : The median number of genes detected per cell-associated barcode.

Saturation : The fraction of UMI originating from an already-observed UMI. There is a difference in how CeleScope and CellRanger calculate saturation. CeleScope shows umi_saturation in the report, while CellRanger shows read_saturation in the report. For details, see here. read_saturation: 28.98%.